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Final Exam BIS 105 Prof. T. Murphy June 7, 2014 This exam has 9 essay questions and 30 multiple-choice questions. Exam instructions (1) Write your name on the top of this page and every page of the essay portion of the exam. (2) Show all work for full credit. (3) If you need more space, continue on the back of the same page (label the question). (4) There is a Scantron section to the exam. It is essential that you write your name and student ID number on the Scantron form and FILL IN THE ID NUMBER BOXES and Test Form A. Please read and sign the statement below: Honor code statement My signature below affirms that I wrote this exam in the spirit of the honor system of UCD. I neither received nor furnished any help during the exam. Signature ________________________________________ The following formulas and constants might be helpful: V = Vmax [S]/([S]+Km) V = (Vmax/(1 + [I]/Ki))[S] ([S] + Km) V = Vmax[S] . ([S] + Km(1 + [I]/Ki)) ΔG’ = RT ln ([product]/[reactant]) + z F ΔEo’ ΔG’ = -2.3 RT ΔpH + z F ΔEo’

ΔG’ = ΔGo’ + RT ln ([Y]/[X]) pH = -log([H+])

ΔGo = -RT ln Keq

ΔGo’ = -nF ΔEo’

ΔE’ = ΔEo’ + (RT/nF )ln([ox]/[red]) A = - log (I/Io) R = 8.31 J/oK-mol F = 96485 J/volt-mol pH = pKa + log([A-]/[HA]) ΔG = ΔE - TΔS

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Scores Question Possible Score

1 12

2 12

3 9

4 12

5 14

6 12

7 12

8 9

9 8

Essay

total 100

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1. (a) (9 pts) Describe the reaction catalyzed by α-ketoglutarate dehydrogenase, showing the structures (and names) of the principal substrates and products. (Show letters for atoms.)

(b)(3 pts) α-ketoglutarate dehydrogenase has a structure similar to that of pyruvate dehydrogenase. Name the three cofactors that contribute to the enzyme's function without being taken up or released from the enzyme. TPP: thymine pyrophosphate (1 pt each) Lipoic acid FAD: flavine adenine dinucleotide 2. A balanced equation for the oxidation of glucose, considering glycolysis, pyruvate dehydrogenase and the TCA cycle, but not electron transport, is: C6H12O6 + 10 NAD+ + 2 FAD + 6 H2O + 2 ADP + 2 GDP + 4 Pi

6 CO2 + 10 NADH + 10 H+ + 2 FADH2 + 2 ATP + 2 GTP + 4 H2O (a)(4 pts) Write a similar equation for the oxidation of pyruvic acid. C3H4O3 + 4 NAD+ + FAD + (GDP + Pi) + 2 H2O 3 CO2 + 4 (NADH + H+) + FADH2 + GTP (b)(4 pts) What is the yield of ATP that you would expect from the oxidation of the NADH + H+ and FADH2 that you show is produced by the oxidation of pyruvic acid. (Show your calculations.) 4 NADH + H+: (4)(2.5) = 10 ATP Total: 11.5 ATP 1 FADH2 : (1)(1.5) = 1.5 ATP (c)(4 pts) Explain the assumptions that you made in answering part (b) with regard to proton transport and the structure of the ATP synthase. Assume 10 H+ per NADH, 6 H+ per FADH2 (2 pts each assumption) Assume 12 subunits in F0, 4 H+ per ATP (other assumptions OK if they fit part (b))

Substrate: 3 pts Product: 3 pts NAD+/NADH: 1 pt -CO2: 1 pt CoASH: 1 pt

-1 pt for each omitted or incorrect factor

+2 pts for each number (with factors)

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3. (a) (6 pts) Given the standard electrochemical potentials for the following reactions, NAD+ + 2H+ + 2e- ---> NADH + H+ - 0.320 V ½ O2 + 2H+ + 2e- ---> H2O +0.816 V and assuming standard conditions (1 M substrates and products), calculate the free energy available to make ATP from the oxidation of NADH. Give units! ΔGo’ = -nF ΔEo’ = -2(96,485)(1.136) = -219,214 J/mol (-219 kJ/mol) (2 pts for formula; 2 pts for correct answer; 2 pts for units ) (b) (3 pts) Calculate the additional change in energy available to make ATP if the ratio of [NADH]/[NAD+] is 10/1. ΔGo’ = RT ln([ox]/[red]) = (8.3)(298) ln(1/10) = (8.31)(298)(-2.3) = -5,695 J/mol (-5.7 kJ/mol) (2 pts for formula; 1 pts for correct answer; total with (a) OK) 4. In the liver, glycogen synthesis generally occurs when cells have plenty of energy. (a)(4 pts) Name enzymes of gluconeogenesis that function when a cell has a high energy level (or diagram their reactions). Pyruvate carboxylase 1 pt each PEP carboxykinase Fructose-1,6-bisphosphatase Glucose-6-phosphatase (b)(2 pts) Name the substrate that is directly involved in the addition of one glucose to a growing glycogen chain. UDP-glucose (uridinediphosphoglucose) (c)(6 pts) How much energy (in terms of ATP ADP equivalents) is required to add one glucose to a growing glycogen chain? Explain. The total is 2: 1 ATP for glc + ATP glc-6-P + ADP 1 ATP equivalent for glc-1-P + UTP UDPG + PPi, PPi + H2O 2 Pi glycogenn-1 + UDPG glycogenn + UDP (2 pts for total (2), 2 for glc-6-P, 2 for UDPG)

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5. (a)(5 pts) Identify the labeled boxes in the figure above: A (a compound)___H2O___ B (a compound)___NADPH________ X (name represented by the wavy line) __photons (quanta, light)__ Y (collection of proteins)____PSII (photosystem II)_____ Z (collection of proteins) ____PSI (photosystem I)____________ (b) (6 pts) Using the "Reduction potential" values on the ordinate of the graph (and equations from the front of the exam), estimate the free energy provided by "P680" and "P700" and the free energy saved by the transport of one electron from "A" to "B". P680: ΔEo = -0.8 - 1.0 = -1.8 V This is volts invested; volts available, + 1.8 V

ΔGo = -(1)(96485)(1.8) = -173 kJ/mol (-173,673 J/mol) P700: ΔEo = -1.4 - 0.4 = -1.8 V This is volts invested; volts available, + 1.8 V

ΔGo = -(1)(96485)(1.8) = -173 kJ/mol (-173,673 J/mol) (P700 may provide ~5% less energy than P680 if both absorb their peak wavelengths.)

G(B) - G(A): ΔEo = -0.4 - 0.8 = -1.2 V This is volts invested; available, + 1.2 V ΔGo = -(1)(96485)(1.2) = -116 kJ/mol (-116,782 J/mol)

(c) (3) Explain the difference between the energy provided and the energy saved, as described by your values in part (b). The difference represents in part the energy used to make ATP and in part energy lost as heat (or the free energy change that must occur for the reactions to proceed spontaneously). 2 pts for either answer along; 3 pts for both

X

X

Y Z

B

A

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6. (a)(10 pts) Diagram the missing intermediate in the (partial) pathway shown below.

(b) (2 pts) In this pathway, the source of the NADPH is _pentose phosphate pathway (PPP)_. 7. (3 pts each part) How many molecules of the following compounds are obtained from the ß-oxidation of myristic acid (14C)(not including reactions of the TCA cycle)? Show calculations. a). NADH + H+ 6: for the 6 acetyl-CoAs reduced and removed b). FADH2 6: for the 6 acetyl-CoAs reduced and removed c). Acetyl-CoA 7: for the 6 acetyl-CoAs reduced and removed plus the one left over d). ATP (consider use in the activation of the myristic acid) 2 (ATP AMP + PPi; ATP + AMP 2 ADP)

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8. (a)(2 pts) Draw the structure of urea. 2 pts: H2N-C-NH2 || O (b)(7 pts) Explain how N from excess amino acids (for instance, leucine) can be removed from the body through transamination and the urea cycle. (4 pts) Amino acid + fumarate --(transamination) a-keto acid + aspartate (3 pts) Aspartate is an intermediate of the urea cycle. 9. (8 pts) Fill in the blanks for the specific cellular location in animal cells for the metabolic pathways below: A. Gluconeogenesis occurs in the _______cytoplasm_(+ mitochondrion)_____

B. Fatty acid synthesis occurs in the ____________cytoplasm______________

C. The TCA cycle occurs in the _____________mitochondrion____________

D. The urea cycle occurs in the ________cytoplasm_(+ mitochondrion)______

E. Glycolysis occurs in the ________________ cytoplasm________________

F. The electron transport chain occurs on the _cristae of the mitochondrion___

G. The Pentose Phosphate Pathway occurs in the ______cytoplasm__________

H. Fatty acid oxidation occurs in the _______mitochondrion_______________

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1. Which of the following elements is not an essential component of proteins (i.e, not a component of one of the 20 standard amino acids)? a. carbon b. nitrogen c. phosphorus d. sulfur e. hydrogen 2. For any biochemical reaction, the equilibrium constant (Keq) is directly proportional to … a. ΔG' b. ΔGo' c. ln(ΔG') d. e-ΔGo'/RT e. ΔS 3. The pKa of acetic acid is 4.76. In a solution of 0.2 M acetic acid that has been adjusted to pH 4.76 with a strong base (KOH or NaOH), the concentration of acetate ion will be… a. 0.1 M b. 0.2 M c. 0 M d. 0.05 M e. The concentration will depend on which base was used. 4. The pKa1 for the dissociation of succinic acid to succinate(-1) is 4.21; the pKa2 for the dissociation of succinate(-1) to succinate(-2) is 5.63. The pH of a solution of 0.1 M Na succinate (without any additional acid or base) will be… a. 4.21 b. 4.92 c. 5.21 d. 0 e. 14 5. The amino acid shown at the right is… a. cysteine b. methionine c. leucine d. lysine e. arginine

6. Consider an enzyme in solution in the cytoplasm of a cell. Where in this enzyme will an amino acid residue with the side chain shown in problem 5 normally be found ? a. at the surface b. at the N-terminal end c. at the C-terminal end d. buried in the center e. any of the foregoing places 7. In general, dissolving a purified enzyme in a solution at a basic pH (e.g., pH 12) will cause it to denature. Among the following bonds, those least likely to break at this pH are… a. hydrogen bonds b. Van der Waal's interactions c. disulfide bonds d. electrostatic attractions e. hydrophobic interactions

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8. You are purifying an enzyme. After step 3, your solution had a total activity of 1000 units and a specific activity of 200 units/mg. After step 4, your solution had a total activity of 500 units and a specific activity of 500 units/mg. Which of the following statements is clearly true? a. In step 4, you lost one-half of your enzyme and 80% of the total protein. b. In step 4, you gained 2.5 times more enzyme than you started with. c. After step 4, your enzyme was pure. d. If you had skipped step 3 and went directly to step 4, you would have obtained the same specific activity. e. None of the above statements is clearly true. 9. The low-barrier-hydrogen-bond that contributes to the enzymatic activity of chymotrypsin… a. involves a bond between an aspartic acid and a histidine in the enzyme. b. involves a bond between an aspartic acid in the enzyme and a histidine in the substrate. c. involves a bond between an aspartic acid in the enzyme and a phenylalanine in the substrate. d. raises the activation energy needed to catalyze the reaction. e. is involved in the enzymatic activity of every type of enzyme. 10. The Michaelis-Menten equation is…

a. ΔG’ = ΔGo’ + RT ln ([Y]/[X]) b. ΔGo = -RT ln Keq c. pH = pKa + log([A-]/[HA]) d. V = Vmax [S]/([S]+Km) e. 1/V = 1/Vmax + (Km/Vmax)(1/[S])

11. The graph at the right describes the kinetics of an enzyme with and without the presence of an inhibitor. The most reasonable conclusion from these data is… a. This enzyme has multiple subunits. b. This graph describes competitive inhibition. c. This graph describes non-competitive inhibition. d. This graph describes uncompetitive inhibition. e. The inhibitor binds to a different site from the substrate.

1/V

1/[S]

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12. In an animal cell, limiting O2 is expected to slow or stop the transport of materials along microtubules. This occurs because kinesin requires… a. one ATP for every step forward. b. two ATPs for every step forward. c. one NAD+ for every step forward. d. two NAD+s for every step forward. e. myosin, and myosin is trapped on actin microfibrils in the absence of ATP. 13. The sugar shown at the right is the ring form of… a. cellobiose b. glucose c. galactose d. fructose e. ribose

14. In a comparison of two membranes, each formed from phosphotidyl choline molecules containing steric and linoleic acid residues, the membrane that retains a liquid crystal form at the lowest temperature will have… a. the highest fraction of steric acid. b. the highest fraction of linoleic acid. c. equal amounts of steric and linoleic acid. d. Since both membranes contain phosphotidyl choline, there will be no difference in the temperature at which they lose their liquid crystal form. 15. Which of the following amino acids would you least expect to find in a membrane-spanning alpha-helix? a. alanine b. arginine c. leucine d. valine e. phenylalanine 16. In general, the formation of a polymer, such as amylose, requires the net hydrolysis of ATP (or UTP, GTP, etc.) because… a. ΔS for the polymerization reaction is positive. b. ΔS for the polymerization reaction is negative. c. ΔE for the formation of the connecting (glycosidic) bond is positive. d. ΔE for the formation of the connecting (glycosidic) bond is negative. e. The formation of a polymer usually just requires an enzyme, not ATP (or UTP, GTP, etc.).

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17. Which of these five enzymes catalyzes a reaction of glycolysis with a strongly negative ΔG? a. enolase b. glyceraldehyde-3-P dehydrogenase c. triose-P isomerase d. citric synthase e. phosphofructokinase 18. Consider yeast cells growing in a vat of stagnant grape juice. For every glucose molecule that they metabolize anaerobically, they will synthesize (net)… a. one molecule of ATP and one molecule of lactate. b. two molecules of ATP and two molecules of lactate. c. four molecules of ATP and four molecules of lactate. d. two molecules of ATP and one molecule of lactate. e. one molecule of ATP and two molecules of lactate. 19. Which of these mitochondrial enzymes does not synthesize NADH? a. isocitric dehydrogenase b. a-ketoglutarate dehydrogenase c. succinic dehydrogenase d. malate dehydrogenase e. pyruvate dehydrogenase 20. For the reaction, malate + NAD+ oxalacetate + NADH + H+, ΔEo' = -0.154 V. This means that under standard conditions, the reaction will proceed… a. forward. b. backward. 21. The mitochondrial electron transport system couples the oxidation of one mole of NADH and reduction of ½ mole of O2 to the … a. synthesis of two moles of phosphoglyceric acid. b. direct synthesis of one mole of ATP. c. direct synthesis of three moles of ATP. d. transport of 10 moles of H+ into the mitochondrial matrix. e. transport of 10 moles of H+ out of the mitochondrial matrix. 22. Direct measurements suggest that in some bacteria, the oxidation of one mole of NADH by ½ mole of O2 provides energy for the synthesis of 2.0 moles of ATP. In animal cells, the P/O ratio is 2.5. Assuming that the electron transport chain in the bacteria transport 10 moles of H+ per mole of NADH oxidized, the 2.0 P/O ratio is best explained by the assumption that… a. the head (F1 component) of the ATP synthase has four subunits. b. the head (F1 component) of the ATP synthase has five subunits.

c. the collar (F0 component) of the ATP synthase has 10 subunits. d. the collar (F0 component) of the ATP synthase has 15 subunits. e. These results cannot be explained by the structure of the ATP synthase.

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23. In a plant chloroplast, how many photons are required for the reduction of one NADP+ to NADPH? a. 1 b. 2 c. 2.5 d. 4 e. 8 24. Which of the listed biochemical pathways is important for providing the reducing power needed for the synthesis of fatty acids? a. pentose phosphate pathway b. glycolysis c. tricarboxylic acid cycle d. gluconeogenesis e. mitochondrial electron transport chain 25. Gluconeogenesis differs from glycolysis at three steps: three enzymes of glycolysis are replaced by four enzymes in gluconeogenesis. Which enzyme in the list below is specifically for gluconeogenesis (and not glycolysis)? a. phosphofructokinase b. enolase c. glyceraldehyde-P dehydrogenase d. pyruvate kinase e. fructose-1,6-bisphosphatase 26. The oxidation of steroyl-CoA (18C) to palmitoyl-CoA (16C) will yield... a. one NADH, one FADH2, and one acetyl-CoA b. one NADH, one FADH2, one ATP, and one acetyl-CoA. c. two H2O and one acetyl-CoA.

d. two NADH and two acetyl-CoA. e. two NADPH and one acetyl-CoA.

27. The formation of palmitoyl-CoA (C16) from myristoyl-CoA (C14) will involve... a. one malonyl-CoA, one NADH, and one FADH2. b. one malonyl-CoA, one NADH, one FADH2, and one ATP. c. one malonyl-CoA and two H2O.

d. one malonyl-CoA and two NADH. e. one malonyl-CoA and two NADPH. 28. The urea cycle provides a pathway for the elimination of excess nitrogen from the body. Which amino acid directly contributes one of the nitrogen atoms found in urea? a. glutamate b. glycine c. aspartate d. alanine e. tryptophan

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29. Two “coupled reactions” will proceed if and only if ... a. the sum of the ΔGs of the two reactions is zero. b. the sum of the ΔGs of the two reactions is positive. c. the sum of the ΔGs of the two reactions is negative. d. the ΔG of the endergonic reaction is negative. e. they are both redox reactions with the same ΔEo.

30. In pure water at pH 7, the concentration of OH- ions is… a. 0 M b. 10-0 = 1 M c. 10-7 M d. 7 M e. undetermined